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Recently a number of advances have been implemented into the core

Recently a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process reduce costs or improve data resolution. Ridaforolimus separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data increasing confidence in peak identification and allowing for motif searching but also afforded discovery of a novel CTCF binding motif. INTRODUCTION ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) has emerged as a powerful and widely used methodology for defining the site-specific localization of transcription factors and histone marks in the context of the cellular genome (1-3). Since inception of this core technique nearly a decade ago several improvements have been implemented to expand the capabilities (4-11) reduce costs (12 13 TLR3 or maximize resolution (14-16). In many of the recently enhanced ChIP-based methods including ChIP-exo ChIP-nexus lobChIP and ChIPmentation (12-15) several steps of sample and/or library preparation are performed on bead-bound immunoprecipitated chromatin posing a challenge in generating a similarly treated input control required for downstream bioinformatic analysis and data quality assessments. Numerous reports have focused on the sources Ridaforolimus and methods for removal of artifacts in ChIP-based data units many of which spotlight the necessity and critical importance of having a proper input control (2 17 For ChIP-seq input controls are normally derived from isolated cellular DNA that has been cross-linked sheared Ridaforolimus and ideally chemically treated in an analogous manner to DNA immunoprecipitated for the protein of interest. When subjected to high-throughput sequencing in parallel with the ChIP sample the input control informs around the genomic locations of technique-specific artifact peaks that exist in the ChIP-seq data set. As such the use of an input control has become a core component of the communally agreed upon standards and guidelines for ChIP-seq experiments (20). In lieu of using a comparable input less ideal methods for artifact removal must be implemented such as: (i) utilizing an IgG control which typically pulls-down comparably less Ridaforolimus DNA resulting in lower library complexity and significant sequencing biasing relative to the ChIP sample (19 20 Ridaforolimus (ii) relying on only filtering ChIP-seq derived blacklisted peaks which is unable to eliminate technique-specific false positives; and/or (iii) applying option peak caller strategies in which binding motifs. Here we report a method for nonspecifically capturing cross-linked chromatin complexes via protein carboxylate groups that allows for the DNA to be subjected to all downstream chemical treatments in parallel with bead-bound chromatin separately immunoprecipitated for the target of interest. This input control method termed protein attached chromatin capture (PAtCh-Cap) is designed to be facile and universally relevant to any of the current (12-15) and future ChIP-based techniques that perform additional chemical and library preparation actions on bead-bound chromatin. Applying our input control method to the analysis of CTCF ChIP-exo data exhibited that we were able to selectively remove artifacts in both pericentromeric and gene proximal regions significantly increasing confidence in peak identification exposing previously unidentifiable peaks and affording the capability of performing a motif search analysis. This improved analysis capability within a high-resolution ChIP-exo data set was essential for the identification of a novel CTCF motif that appears to have an independent cellular function. MATERIALS AND METHODS Cell culturing HeLa cells (from your laboratory of Prof. C.J. Burrows; University or college of Utah) were cultured in Dulbecco’s altered Eagle medium supplemented with 4.5 g/l glucose 10 fetal bovine serum and 2 mM glutamine and managed in a humidified incubator at 37°C and 5% CO2. Cell counting and viability analysis was performed on a Countess Automated Cell Counter (Thermo Fisher Scientific). Cell collection authentication to confirm lack of cross-contamination was routinely verified by short tandem repeat (STR) DNA profiling..